A new system for naming ribosomal proteins

doi:10.1016/j.sbi.2014.01.002

Review

. 2014 Feb:24:165-9.

doi: 10.1016/j.sbi.2014.01.002. Epub 2014 Feb 10.

A new system for naming ribosomal proteins

Nenad Ban¹, Roland Beckmann², Jamie H D Cate³, Jonathan D Dinman⁴, François Dragon⁵, Steven R Ellis⁶, Denis L J Lafontaine⁷, Lasse Lindahl⁸, Anders Liljas⁹, Jeffrey M Lipton¹⁰, Michael A McAlear¹¹, Peter B Moore¹², Harry F Noller¹³, Joaquin Ortega¹⁴, Vikram Govind Panse¹⁵, V Ramakrishnan¹⁶, Christian M T Spahn¹⁷, Thomas A Steitz¹⁸, Marek Tchorzewski¹⁹, David Tollervey²⁰, Alan J Warren¹⁶, James R Williamson²¹, Daniel Wilson²², Ada Yonath²³, Marat Yusupov²⁴

Affiliations

¹ Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 30, 8093 Zurich, Switzerland.
² Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen Str. 25, University of Munich, 81377 Munich, Germany.
³ Department of Chemistry, University of California, Berkeley, CA 94720, USA.
⁴ Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
⁵ Département des sciences biologiques and Centre de recherche BioMed, Université du Québec à Montréal, Montréal, Québec, Canada.
⁶ Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA.
⁷ RNA Molecular Biology, FRS/F.N.R.S., Université Libre de Bruxelles, Charleroi Campus, B-6041 Charleroi, Belgium.
⁸ Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
⁹ Biochemistry and Structural Biology, Lund University, Åkeröv 26, SE-793 Leksand, Sweden. Electronic address: anders.liljas@mbfys.lu.se.
¹⁰ Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, USA; Hofstra School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA.
¹¹ Molecular Biology and Biochemistry Department, Wesleyan University, 237 Church St., Middletown, CT 06459, USA.
¹² Department of Chemistry, Yale University, PO Box 208107, New Haven, CT 06520, USA. Electronic address: peter.moore@yale.edu.
¹³ Department of MCD Biology, UCSC, Santa Cruz, CA 94720, USA.
¹⁴ Department of Biochemistry and Biomedical Sciences, DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
¹⁵ Institute for Biochemistry, ETH Zurich, HPM F12.2, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland.
¹⁶ MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
¹⁷ Institut für Medizinsche Physik und Biophysik, Charite-Universitätsmedizin, Ziegelstrass 5-6, 10117 Berlin, Germany.
¹⁸ Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA.
¹⁹ Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
²⁰ Welcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
²¹ Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
²² Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
²³ Structural Biology Department, Weizmann Institute of Science, Rehovot 76100, Israel.
²⁴ Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. Electronic address: marat@igbmc.u-strasbg.fr.

PMID: 24524803
PMCID: PMC4358319
DOI: 10.1016/j.sbi.2014.01.002

Review

A new system for naming ribosomal proteins

Nenad Ban et al. Curr Opin Struct Biol. 2014 Feb.

. 2014 Feb:24:165-9.

doi: 10.1016/j.sbi.2014.01.002. Epub 2014 Feb 10.

Authors

Affiliations

¹ Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 30, 8093 Zurich, Switzerland.
² Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen Str. 25, University of Munich, 81377 Munich, Germany.
³ Department of Chemistry, University of California, Berkeley, CA 94720, USA.
⁴ Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
⁵ Département des sciences biologiques and Centre de recherche BioMed, Université du Québec à Montréal, Montréal, Québec, Canada.
⁶ Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA.
⁷ RNA Molecular Biology, FRS/F.N.R.S., Université Libre de Bruxelles, Charleroi Campus, B-6041 Charleroi, Belgium.
⁸ Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
⁹ Biochemistry and Structural Biology, Lund University, Åkeröv 26, SE-793 Leksand, Sweden. Electronic address: anders.liljas@mbfys.lu.se.
¹⁰ Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, USA; Hofstra School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA.
¹¹ Molecular Biology and Biochemistry Department, Wesleyan University, 237 Church St., Middletown, CT 06459, USA.
¹² Department of Chemistry, Yale University, PO Box 208107, New Haven, CT 06520, USA. Electronic address: peter.moore@yale.edu.
¹³ Department of MCD Biology, UCSC, Santa Cruz, CA 94720, USA.
¹⁴ Department of Biochemistry and Biomedical Sciences, DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
¹⁵ Institute for Biochemistry, ETH Zurich, HPM F12.2, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland.
¹⁶ MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
¹⁷ Institut für Medizinsche Physik und Biophysik, Charite-Universitätsmedizin, Ziegelstrass 5-6, 10117 Berlin, Germany.
¹⁸ Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA.
¹⁹ Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
²⁰ Welcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
²¹ Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
²² Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
²³ Structural Biology Department, Weizmann Institute of Science, Rehovot 76100, Israel.
²⁴ Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. Electronic address: marat@igbmc.u-strasbg.fr.

PMID: 24524803
PMCID: PMC4358319
DOI: 10.1016/j.sbi.2014.01.002

Abstract

A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names.

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References

1. Wittmann HG, Stoeffler G, Hindennach I, Kurland CG, Randall-Hazelbauer L, Birge EA, Nomura M, Kaltschmidt E, Mizushima S, Traut RR, et al. Correlation of 30S ribosomal proteins of Escherichia coli isolated in different laboratories. Mol Gen Genetics. 1971;111:327–333. - PubMed
1. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjuro A, Holton JH, Doudna Cate JH. Structure of the bacterial ribosome at 3.5 A resolution. Science. 2005;310:827–834. - PubMed
1. Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000;407:327–339. - PubMed
1. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001;292:883–896. - PubMed
1. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001;107:679–688. - PubMed

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[1] Wittmann HG, Stoeffler G, Hindennach I, Kurland CG, Randall-Hazelbauer L, Birge EA, Nomura M, Kaltschmidt E, Mizushima S, Traut RR, et al. Correlation of 30S ribosomal proteins of Escherichia coli isolated in different laboratories. Mol Gen Genetics. 1971;111:327–333. - PubMed

[2] Wittmann HG, Stoeffler G, Hindennach I, Kurland CG, Randall-Hazelbauer L, Birge EA, Nomura M, Kaltschmidt E, Mizushima S, Traut RR, et al. Correlation of 30S ribosomal proteins of Escherichia coli isolated in different laboratories. Mol Gen Genetics. 1971;111:327–333. - PubMed

[3] Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjuro A, Holton JH, Doudna Cate JH. Structure of the bacterial ribosome at 3.5 A resolution. Science. 2005;310:827–834. - PubMed

[4] Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjuro A, Holton JH, Doudna Cate JH. Structure of the bacterial ribosome at 3.5 A resolution. Science. 2005;310:827–834. - PubMed

[5] Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000;407:327–339. - PubMed

[6] Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000;407:327–339. - PubMed

[7] Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001;292:883–896. - PubMed

[8] Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001;292:883–896. - PubMed

[9] Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001;107:679–688. - PubMed

[10] Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001;107:679–688. - PubMed

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A new system for naming ribosomal proteins

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A new system for naming ribosomal proteins

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